Changelog
1.2 (2025-03-31)
PACKAGE: SHIMMING TOOLBOX
BUG
Update tutorials. View pull request
ENHANCEMENT
st_b0shim: Use the table position information to generate spherical harmonic coil profiles with proper origin. View pull request
st_b0shim: Allow the use of order 1 or 0 by themselves when using output format of 'gradient'. View pull request
st_b0shim: Add the ability to set the current shim coefficient values as inputs in the constraint file. View pull request
st_dicom_to_nifti: Add MPRAGE to recognized files. View pull request
FEATURE
st_b0shim: Add CLI to combine text files. View pull request
st_b0shim: Add signal loss optimization to RMSE criteria. View pull request
st_download_data, st_mask: Automatic mask creation for MRS shimming based on voxel position . View pull request
st_maths: Compute phase and magnitude images from real/imaginary data. View pull request
PACKAGE: PLUGIN
FEATURE
st_b0shim: Add signal loss optimization to RMSE criteria. View pull request
REPO
TESTING
Update GitHub Actions to more recent versions. View pull request
1.1 (2024-11-08)
PACKAGE: SHIMMING TOOLBOX
ENHANCEMENT
st_b0shim, st_dicom_to_nifti: Update dcm2bids config file for Philips and output JSON sidecar for the calculated field maps. View pull request
BUG
st_b0shim: Update signal recovery calculation. View pull request
st_dicom_to_nifti: Fix default dcm2bids config file not existing on Windows installation. View pull request
REPO
ENHANCEMENT
Create a workflow to automate updating CHANGES.md. View pull request
BUG
Fix test issues coming from incompatibility with fsl bet2. View pull request
DOCUMENTATION
Update documentation configuration file to support ReadTheDocs addons migration. View pull request
1.0 (2024-08-21)
PACKAGE: SHIMMING TOOLBOX
FEATURE
st_b0shim: Add shim CLI and sequencer. View pull request
st_b0shim: Implement order 2 in st_b0shim static and realtime CLI. View pull request
st_b0shim: Deal with saturation pulse when B0 shimming. View pull request
st_b0shim: Add standard deviation criteria and options to select it in st_b0shim CLI. View pull request
st_b0shim: Implement maximization of shim settings based on signal intensity. View pull request
st_b0shim: Signal recovery optimizer. View pull request
st_b0shim: Faster B0 shimming by changing some mathematical expressions. View pull request
st_b0shim: Add compatibly for Philips scanners. View pull request
st_b0shim: Changed the optimizer to a quadratic problem. View pull request
st_b0shim: Add GE compatibility, spherical harmonic shim + refactoring of the Scanner shim coordinate systems. View pull request
st_b1shim: Added argument for VOP path in b1shim cli. View pull request
st_b1shim: Improve B1 shimming: implement resampling of masks into B1 maps + phase only shimming and add documentation. View pull request
st_check_dependencies, st_mask: first iteration to adding BET. View pull request
st_create_coil_profiles: Implement coil profile generation API/CLI. View pull request
st_create_coil_profiles: Coil profiles creation from CAD geometries. View pull request
st_create_coil_profiles: Add CLI and GUI command to create constraint files. View pull request
st_mask: Add a cli to create a spherical mask. View pull request
st_prepare_fieldmap: Use --savemask option from prelude to calculate the output mask in st_prepare_fieldmap. View pull request
st_prepare_fieldmap: Multi echo field mapping. View pull request
st_prepare_fieldmap: Implement skimage's phase unwrapper. View pull request
st_realtime_shim: Add realtime sequencing ability. View pull request
st_sort_dicoms: Add a CLI to sort DICOMs in separate folders. View pull request
st_unwrap: Add unwrap CLI. View pull request
ENHANCEMENT
st_b0shim: Add gradient shimming output file format to the b0 static CLI. View pull request
st_b0shim: Resample input masks on the target anat when B0 shimming. View pull request
st_b0shim: Parse slice ordering from BIDS json sidecar. View pull request
st_b0shim: Reduce memory usage and speed things up when shimming. View pull request
st_b0shim: Add fatsat option in dynamic and realtime dynamic b0shimming. View pull request
st_b0shim: Allow 4d masks and target anatomical when using dynamic shimming. View pull request
st_b0shim: Use multiprocessing's fork method to speed up optimizing. View pull request
st_b0shim: Create output directory automatically for st_b0shim max-intensity. View pull request
st_b0shim: Log the indexes when using st_b0shim max-intensity. View pull request
st_b0shim: Faster B0 shimming . View pull request
st_b0shim: Add ability to shim using 2D field maps. View pull request
st_b0shim: Make Resampling faster by using multiprocessing with joblib. View pull request
st_b0shim: Changed the optimization to get faster results. View pull request
st_b0shim: Improve real-time shimming. View pull request
st_b0shim: Shimmed field map plotting for real time shimming by averaging over time dimension. View pull request
st_b0shim: Split coils and scanner order for optimization + allow specific scanner orders for each. View pull request
st_b0shim: Add 3rd order spherical harmonics. View pull request
st_b0shim: Implement Philips+GE related spherical harmonics conventions. View pull request
st_b0shim, st_image: Improve output of st_b0shim and add st_image logical-and. View pull request
st_b1shim: Implement RF shimming code. View pull request
st_b1shim: Improved RF shimming output figure. View pull request
st_b1shim: Add norm constraint to shim-weights when not SAR constrained. View pull request
st_b1shim: Minor improvements of B1+ shimming functionalities. View pull request
st_b1shim: Add regularization term to CV reduction. View pull request
st_b1shim: Real/imaginary B1+ shim weights splitting instead of magnitude/phase. View pull request
st_b1shim: Add output B1 shim weights as a machine friendly text file. View pull request
st_b1shim, st_dicom_to_nifti: Fix B1+ maps right after their conversion into NIfTI. View pull request
st_create_coil_profiles: Add ability to input a mask when creating coil profiles. View pull request
st_dicom_to_nifti: Add output of phase for anat images in dcm2bids. View pull request
st_dicom_to_nifti: Improve dcm2bids config file and fieldmap conversion. View pull request
st_dicom_to_nifti: Add verbose to the st_dicom_to_nifti. View pull request
st_dicom_to_nifti: Add mp2rage, and more field maps to dcm2bids config file and update to version >= 2.1.7. View pull request
st_dicom_to_nifti: New dcm2bids config file. View pull request
st_download_data: Update link to the newest version of the coil profile tutorial. View pull request
st_image: Resample in logical-and if the volumes are not the same orientation. View pull request
st_mask: Update nibabel to latest version and allow to input a scaled threshold. View pull request
st_prepare_fieldmap: Update prepare_fieldmap CLI/API to accept non siemens data more easily. View pull request
st_prepare_fieldmap: Correct for possible 2*pi offsets across time points when unwrapping. View pull request
st_prepare_fieldmap: Add option to save the calculated mask when using st_prepare_fieldmap. View pull request
st_sort_dicoms: Allow to sort any DICOM files. View pull request
st_sort_dicoms: Add recursive option to sort dicoms. View pull request
Handling of different slice orientation when reading b1 maps. View pull request
Added handling of coronal RF nifti + tests for all orientations. View pull request
Allow spaces in the CLIs. View pull request
Changed version of matplotlib. View pull request
Add ability to simulate x, y and z gradients. View pull request
BUG
st_b0shim: Fix bug where there were dead voxels in the calculated shim figures. View pull request
st_b0shim: Improve mask resampling. View pull request
st_b0shim: Invert polarity of the frequency adjust. View pull request
st_b0shim: Fixed a particular case, when there is nothing to shimmed in an optimization. View pull request
st_b0shim: Solved a bug where mask_fmap and the dilated mask where switched. View pull request
st_b0shim: Fix an issue where real-time shimming would not work using pseudo-inverse. View pull request
st_b0shim: Resolve quadrog issue when the sum of the channels constraint was infinite. View pull request
st_b0shim: Bug fix: "absolute" output format. View pull request
st_b0shim: Update custom coil config file. View pull request
st_b0shim: Update how constraints are handled. View pull request
st_b0shim: Change erode to dilate for optimization. View pull request
st_b0shim: Fix a bug when scanner constraints are not implemented. View pull request
st_b0shim, st_mask, st_prepare_fieldmap: Fix st_b0shim realtime-dynamic order 0 and output folder for masking and fieldmap. View pull request
st_check_dependencies: Change command that checks for sct installation. View pull request
st_check_dependencies: Change SCT CLI call to check version. View pull request
st_dicom_to_nifti: Fix phasediff renaming issue for dual-echo fieldmaps. View pull request
st_dicom_to_nifti: Update dcm2bids to version 3.0.1. View pull request
st_dicom_to_nifti: Improve reliability of phase diff renaming. View pull request
st_dicom_to_nifti: Solve dcm2niix not in PATH issue and improve st_prepare_fieldmap documentation. View pull request
st_dicom_to_nifti, st_prepare_fieldmap: Bug fix related to updating FSLeyes version and Shimming Toolbox version. View pull request
st_download_data: Fix broken link in st_download_data data_create_coil_profiles. View pull request
st_prepare_fieldmap: Field mapping pipeline improvement. View pull request
st_prepare_fieldmap: Resolve prelude error if --savemask directory is not already created when field mapping. View pull request
st_prepare_fieldmap: Change phase range in field mapping calculations. View pull request
st_realtime_shim: Fix realtime shimming mask resampling modes. View pull request
st_realtime_shim: gradient realtime shim output coordinate system. View pull request
st_realtime_shim: Gradient realtime_shim orientation and nan problems. View pull request
Solve launchers needing to be launched from the ST venv. View pull request
INSTALLATION
Automate the install process. View pull request
Remove the need for sudo in the installer. View pull request
Update pillow and numpy due to Github security alert. View pull request
Resolve deprecated warnings for np.float. View pull request
Update required importlib-metadata version. View pull request
Share a single conda environment.. View pull request
Switch to using mambaforge. View pull request
Add windows compatibility. View pull request
REFACTORING
st_b0shim: Improve dynamic B0 shimming workflow. View pull request
st_b0shim: Refactoring of the B0 shimming. View pull request
st_b1shim: Reorganizeb1 shimming files. View pull request
st_dicom_to_nifti: Update st_dicom_to_nifti help. View pull request
st_prepare_fieldmap: Updates fieldmapping APIs/CLIs to output proper NIfTI. View pull request
Adapt CI tests to updated testing data organization. View pull request
Replace remaining paths by fname. View pull request
TESTING
st_b1shim: Add unit test for unknown RF shimming algorithm. View pull request
Add missing prelude test marker. View pull request
DOCUMENTATION
st_b1shim: Specify in docstring that CV reduction favors high B1+ efficiency. View pull request
Add versions and a changelog. View pull request
PACKAGE: PLUGIN
FEATURE
st_check_dependencies, st_mask: first iteration to adding BET. View pull request
st_create_coil_profiles: Add CLI and GUI command to create constraint files. View pull request
INSTALLATION
Update to the newest version of Shimming Toolbox [9c454d7]. View pull request
Update ST installation. View pull request
Update wxpython to the latest version. View pull request
Use mamba. View pull request
Share a single conda environment.. View pull request
Share a single conda environment.. View pull request
Bump version and implement features. View pull request
Bump version to include coil profile generation. View pull request
Update version of ST. View pull request
Bump version to include dual-echo field mapping fix. View pull request
Change the version of fsleyes and bump the Shimming Toolbox version. View pull request
Bump Shimming Toolbox version . View pull request
Update fsleyes to 1.12.4. View pull request
ENHANCEMENT
Update installer to integrate with new installer in
shimming-toolbox
. View pull requestGc/b1. View pull request
Fetch CLI docstrings. View pull request
Bump version, implement relevant features and bug fixes. View pull request
Add realtime output of CLIs to fsleyes terminal. View pull request
Implement maximization of shim settings based on signal intensity in the plugin. View pull request
Auto load ST on startup and version bump. View pull request
Adapt GUI to new split optimization. View pull request
Add 3rd order support. View pull request
Ab/signal recovery. View pull request
BUG
Minor bug fixes. View pull request
Improve installation. View pull request
Solve bug preventing to launch Shimming Toolbox on linux. View pull request
Allow to select files from the file dialog box and nested dropdowns. View pull request
bug fix. View pull request
DOCUMENTATION
Add issue template. View pull request
Add pull request template. View pull request
Add LICENSE. View pull request
Add versions and a changelog. View pull request
TESTING
Add continuous integration and pre-commit. View pull request
REFACTORING
Gc/cleanup. View pull request
Major refactoring. View pull request
Merge fsleyes-plugin-shimming-toolbox repo in Shimming Toolbox. View pull request
REPO
ENHANCEMENT
Add GRE-T1w to config file. View pull request
BUG
Update version of read the docs theme. View pull request
Use python 3.10 for windows. View pull request
DOCUMENTATION
add badges to readme for the license and release. View pull request
Improve installation instructions. View pull request
Implement GUI example scenario. View pull request
Simplify installation documentation. View pull request
Add GUI example tuto for b1 shim. View pull request
Update installation documentation. View pull request
Add Siemens compatibility warning to B1+ tutorial. View pull request
Update names of subcommand in the documentation. View pull request
Add information about citation to the documentation. View pull request
Removed unecessary explanations. View pull request
Update b1_shimming.rst. View pull request
Updated documentation to encourage people to post on the forum. View pull request
INSTALLATION
Resolve deprecated st_venv instructions and calls. View pull request
Add windows compatibility. View pull request
Upgrade to python 3.10. View pull request
TESTING
removed ubuntu 16 from test.yml. View pull request
Fix hanging tests in CI. View pull request
Version/python version updates for pre-commit, sklearn and read the docs. View pull request
Change ubuntu 18.04 to 22.04. View pull request
Removed macos-10.15 for 11.0 and 12.0. View pull request
Update GitHub actions to V3. View pull request
Remove macos-11 and add macos-13 in CI. View pull request
0.1 (2021-07-28)
PACKAGE: SHIMMING TOOLBOX
BUG
st_check_dependencies: Refactored prelude and dcm2niix to avoid bug when not on PATH. View pull request
st_dicom_to_nifti: fix remove_tmp argument in dicom_to_nifti. View pull request
Repair dicom_to_nifti missing calls [bug]. View pull request
Update generate meshgrid. View pull request
Fix read_nii not looking for ImageComments and ImageType. View pull request
Fix singleton on last dimension error in prelude. View pull request
Fix local error with load_nifti. View pull request
FEATURE
st_check_dependencies: Check installation and versions of 3rd party binaries. View pull request
st_download_data: Added functions to download data. View pull request
st_image, st_maths: Add ability to average across files. View pull request
st_mask: Add square, cube and threshold cli. View pull request
st_mask: Create CLI for SCT mask. View pull request
st_prepare_fieldmap: Add ability to create fieldmaps. View pull request
st_prepare_fieldmap: eao/gaussian-filter. View pull request
st_realtime_shim: Realtime_zshim shim CLI. View pull request
st_realtime_shim: Output in-plane (x and y) shim coefficients. View pull request
Create numerical model data for multi-echo field maps. View pull request
Add unwrap phase functionality. View pull request
Implement dicom_to_nifti: wrapper for dcm2bids to convert DICOM data. View pull request
Add the ability to load niftis. View pull request
Added masking functionality. View pull request
Implementing basic optimizer and test bench. View pull request
Create synthetic coil-profiles. View pull request
Added API for dealing with coordinate systems. View pull request
Add ability to read from the PMU. View pull request
Add ability to get timing data from scans. View pull request
Updated load_nifti function to handle rf-maps obtained with Turboflash B1 mapping . View pull request
Support fsleyes as a GUI. View pull request
ENHANCEMENT
st_dicom_to_nifti: Update dicom_to_nifti with a CLI. View pull request
st_dicom_to_nifti: Rename phasediff image in dicom_to_nifti. View pull request
st_dicom_to_nifti: Added possibility to identify TFL sequence for rf mapping. View pull request
st_dicom_to_nifti: Update dcm2bids to handle all TFL B1 maps. View pull request
st_mask: Implementation of a test to verify the correct creation of the mask. View pull request
st_prepare_fieldmap: Update prepare fieldmap . View pull request
st_realtime_shim: Add RIRO and Static masks to realtime zshimming. View pull request
st_realtime_shim: optimization by avoiding loops for regression over numpy array.. View pull request
Add a shimming scenario script under /examples. View pull request
Updated general demo script: general_demo.py. View pull request
Added example shell script for realtime z-shimming. View pull request
Optimizing optimizer code to run faster on large fieldmaps with small masks. View pull request
Optimizer improvements. View pull request
Fixed biot-savart scaling. View pull request
Compute gradient in physical and voxel coordinate systems. View pull request
Raise warning when loading RF nifti with missing SliceTiming. View pull request
Refactor and add features to Optimizers. View pull request
TESTING
st_download_data: Update download_data CLI dataset links. View pull request
st_download_data: Updated URL for download data testing. View pull request
st_download_data: Update download data link. View pull request
st_download_data: Updated the testing data release version. View pull request
st_download_data: Update download_data link to the latest release. View pull request
Update dir_testing to be an absolute path. View pull request
Ensure test environment is set up with test data and soft dependencies before running tests. View pull request
Updates link for testing-data. View pull request
REFACTORING
[chore][cli/download_data] Remove stale TODO. View pull request
Remove unneeded example modules. View pull request
Change prelude mag parameter to be an optional argument. View pull request
INSTALLATION
Add basic python package setup. View pull request
packaging: only install tests when asked. View pull request
Upgrade dcm2niix to latest.. View pull request
Moved testing and docs packages in default installation. View pull request
Update minimum version to Python 3.7. View pull request
Update shimming-toolbox package install. View pull request
DOCUMENTATION
Sketch for some command line tools in the toolbox.. View pull request
Source package version from setup.py.. View pull request
[docs][fix] Add documentation dependency installation steps. View pull request
Docstring fixes to address Sphinx build warnings. View pull request
PACKAGE: PLUGIN
FEATURE
Support fsleyes as a GUI. View pull request
REFACTORING
Convert the plugin into a fsleyes package. View pull request
FEATURE
Support fsleyes as a GUI. View pull request
ENHANCEMENT
Add GUI Integration into FSLeyes. View pull request
REPO
DOCUMENTATION
Create CONTRIBUTING.rst and LICENSE. View pull request
Port shimming-toolbox documentation. View pull request
[docs][README] Add RTD build sticker. View pull request
[docs][API reference] Add unwrap module to API reference. View pull request
[docs][API reference] Replace Autodoc with Napoleon. View pull request
[fix][download_data] Automatically generate dataset info in CLI help message. View pull request
Fix link to installation instructions. View pull request
Satisfy GitHub community profile checklist. View pull request
Fixed former repos name. View pull request
Update repo name in documentation and project config files. View pull request
[docs][installation] Add FSL Prelude as dependency. View pull request
Fix RTD badge. View pull request
Add documentation stub for dicom_to_nifti.py. View pull request
Create new CLI documentation section. View pull request
Fix GH Actions badge in README. View pull request
Revised index.rst and leading numbers on RTD directories. View pull request
Add the Twitter badge. View pull request
Update links in README.md. View pull request
Update docs and readme for new dcm2niix version. View pull request
Move images to new repo. View pull request
Update the documentation with up to date info and figures. View pull request
Update documentation. View pull request
Reordered listed 3rd party software, added FSLeyes. View pull request
Added FSLeyes example figure. View pull request
Addition of the commands accessible in shimming-toolbox in the README.rst. View pull request
Update API and CLI documentation. View pull request
TESTING
Install dcm2niix in CI. View pull request
Avoid double-building CI on PRs. View pull request
Fix Travis coveralls post-build step. View pull request
Add ShellCheck to Travis build. View pull request
[need to redo] Add GitHub Actions CI builds. View pull request
Add GitHub Actions CI builds. View pull request
Installation of the SpinalCord Toolbox on GH Actions. View pull request
Remove extraneous workflow. View pull request
Cache SCT in GitHub Actions CI workflow. View pull request
INSTALLATION
ci: Add pre-commit configs. View pull request
CI: Check for correct EOF. View pull request
ci: Check for end-of-line trailing whitespace. View pull request
BUG
Fix coveralls 3.0.0 bug and github actions macos 11.0 bug. View pull request